What timing ... I am in the middle of such a job!
ID every circuit before demolition begins. Many circuits are in sealed off pipes, and are a PITA to identify after the saws-it-all crew chops them off at floor level.
As usual Reno gets in quick and correct!
You imply that the existing service bays and fuel dispensing will continue to be a part of the business and probably while construction is going on.
The existing service is likely inadequate (for what is already there even) and the existing panels something I'd rather not even open to look at let alone be obliged to work in.
Assuming (with all attendant risk) that the new work will require a heavy up... I'd suggest doing it FIRST and if at all humanly possible limit all your work related to re-feeding the old panels to the exterior (trough box etc).
If the AHJ is gonna expect bringing the existing service areas up to code(NEC and fire,etc)... be sure you know it before you start and that your bid reflects it.
